Contacts of the helix formed by residues 516 - 523 (chain I) in PDB entry 5FUR
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLN 516 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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504I LEU* 5.9 8.3 - - + +
515I ILE* 1.3 81.1 - - + +
517I PRO* 1.3 75.3 - - + +
519I ILE* 3.3 7.0 - - - +
520I LYS* 3.0 24.2 + - - +
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Residues in contact with PRO 517 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514I ASP* 3.7 32.8 - - + +
516I GLN* 1.3 98.8 - - + +
518I LEU* 1.3 65.8 + - - +
520I LYS* 3.2 16.2 + - + +
521I GLN* 3.4 20.3 + - - +
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Residues in contact with LEU 518 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459I LEU* 5.6 8.3 - - + -
460I ILE* 4.7 19.5 - - + -
463I ARG* 5.2 14.8 - - + +
514I ASP 4.2 14.5 + - - +
515I ILE* 3.7 7.2 + - + +
516I GLN 3.4 0.8 - - - -
517I PRO* 1.3 77.9 - - - +
519I ILE* 1.3 58.5 + - - +
521I GLN* 2.9 30.0 + - + +
522I TRP* 3.6 40.7 + - + +
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Residues in contact with ILE 519 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368I TRP* 3.7 40.2 - - + +
418I PHE* 5.7 8.7 - - + -
456I VAL* 4.8 10.5 - - + -
515I ILE* 3.2 23.5 + - + +
516I GLN* 3.3 9.4 - - - +
518I LEU* 1.3 76.5 - - - +
520I LYS* 1.4 63.3 + - + +
522I TRP* 2.8 39.2 + - + +
523I VAL* 3.5 17.3 + - + +
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Residues in contact with LYS 520 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516I GLN 3.0 19.3 + - - +
517I PRO* 3.5 10.5 - - + +
518I LEU 3.0 0.6 + - - -
519I ILE* 1.4 74.7 - - + +
521I GLN* 1.3 62.3 + - + +
522I TRP 3.0 6.1 + - - -
523I VAL* 3.0 19.6 + - + +
524I ASP* 2.8 46.8 + - + +
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Residues in contact with GLN 521 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517I PRO* 3.8 13.5 + - - +
518I LEU* 2.9 15.8 + - + +
520I LYS* 1.3 80.0 - - + +
522I TRP* 1.3 72.9 + - + +
526I SER* 3.1 46.3 + - - +
527I GLY 4.0 1.4 + - - -
558I GLN* 5.8 5.9 - - - +
559I LYS 5.4 3.1 + - - +
560I TYR* 3.5 26.4 - - + +
561I VAL 5.7 0.7 + - - -
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Residues in contact with TRP 522 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415I HIS 5.4 2.1 - - - +
417I ILE* 4.7 6.4 + - + +
452I LYS* 3.1 42.6 + - + +
455I LEU* 5.2 3.4 - - + -
456I VAL* 3.6 35.1 - - + +
459I LEU* 3.4 30.9 - - + +
518I LEU* 3.7 39.0 + - + +
519I ILE* 2.8 31.1 + - + +
521I GLN* 1.3 91.6 - - + +
523I VAL* 1.4 64.6 + - + +
524I ASP 3.8 0.4 - - - -
526I SER* 5.8 0.9 - - - -
527I GLY* 5.7 8.1 - - - -
561I VAL 5.9 3.4 - - - -
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Residues in contact with VAL 523 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415I HIS 4.6 1.4 - - - +
416I PRO* 3.1 25.7 - - - +
417I ILE* 3.8 16.6 - - + +
418I PHE* 3.2 52.0 - - + +
519I ILE* 3.8 19.1 - - + +
520I LYS* 3.3 13.5 - - - +
522I TRP* 1.4 86.4 - - + +
524I ASP* 1.3 85.2 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il